fix error due to changed working directory

nf-core · Aug 23, 2022 · 651c629 · 651c629
1 parent 1214af5
commit 651c629
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
@@ -62,10 +62,15 @@ def test_modules_lint_patched_modules(self):
  # Create a patch file
  patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
  patch_obj.patch(BISMARK_ALIGN)
- # change directory to the module directory
+
+ # change temporarily working directory to the pipeline directory
+ # to avoid error from try_apply_patch() during linting
+ wd_old = os.getcwd()
  os.chdir(self.pipeline_dir)
  module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
  module_lint.lint(print_results=False, all_modules=True)
+ os.chdir(wd_old)
+
  assert len(module_lint.failed) == 0
  assert len(module_lint.passed) > 0
  assert len(module_lint.warned) >= 0